{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_CLI"},{"status":"SUCCEEDED","id":"data_set_H"},{"status":"SUCCEEDED","id":"data_set_KI"},{"status":"SUCCEEDED","id":"data_set_N"},{"status":"SUCCEEDED","id":"data_set_V"},{"status":"SUCCEEDED","id":"data_set__CLE"},{"status":"SUCCEEDED","id":"data_set__CLI"},{"status":"SUCCEEDED","id":"data_set__ECL"},{"status":"SUCCEEDED","id":"data_set__EK"},{"status":"SUCCEEDED","id":"data_set__ENA"},{"status":"SUCCEEDED","id":"data_set__KE"},{"status":"SUCCEEDED","id":"data_set__KI"},{"status":"SUCCEEDED","id":"data_set__NAE"},{"status":"SUCCEEDED","id":"data_set__NAI"}],"duration":0.136818,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"},{"status":"SUCCEEDED","id":"curve_2"},{"status":"SUCCEEDED","id":"curve_3"}],"duration":0.217081,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5a320d0> has a label of '_EK vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5a323a0> has a label of '_ENA vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"stiff","key":"meth"},{"value":"200.0","key":"total"},{"value":"0.0","key":"t0"},{"value":"0.2","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000668","duration":0.109444,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.608671,"output":"Archive contains 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 2 plots:\r\n  continuations.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 15 data sets\r\n    Plots (1):\r\n      plot: 3 curves\r\n  time_series.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 17 data sets\r\n    Plots (1):\r\n      plot: 4 curves\r\n\r\nExecuting SED-ML file 1: continuations.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `plot`\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"continuations.sedml"},{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_CLI"},{"status":"SUCCEEDED","id":"data_set_DNK"},{"status":"SUCCEEDED","id":"data_set_H"},{"status":"SUCCEEDED","id":"data_set_KI"},{"status":"SUCCEEDED","id":"data_set_N"},{"status":"SUCCEEDED","id":"data_set_V"},{"status":"SUCCEEDED","id":"data_set__CLE"},{"status":"SUCCEEDED","id":"data_set__CLI"},{"status":"SUCCEEDED","id":"data_set__ECL"},{"status":"SUCCEEDED","id":"data_set__EK"},{"status":"SUCCEEDED","id":"data_set__ENA"},{"status":"SUCCEEDED","id":"data_set__KE"},{"status":"SUCCEEDED","id":"data_set__KI"},{"status":"SUCCEEDED","id":"data_set__MAX_P"},{"status":"SUCCEEDED","id":"data_set__NAE"},{"status":"SUCCEEDED","id":"data_set__NAI"}],"duration":0.160191,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"},{"status":"SUCCEEDED","id":"curve_2"},{"status":"SUCCEEDED","id":"curve_3"},{"status":"SUCCEEDED","id":"curve_4"}],"duration":0.208214,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5bf81f0> has a label of '_EK vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5bf83a0> has a label of '_ENA vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5bf8670> has a label of '_MAX_P vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"stiff","key":"meth"},{"value":"1000.0","key":"total"},{"value":"0.0","key":"t0"},{"value":"1","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000668","duration":3.427418,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":3.94776,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 2 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 2\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 2: time_series.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `plot`\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"time_series.sedml"}],"duration":5.019327,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m========================================== Downloading COMBINE/OMEX archive =========================================\u001b[0m\n  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n                                 Dload  Upload   Total   Spent    Left  Speed\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    471      0 --:--:-- --:--:-- --:--:--   472\n\r100 11817  100 11817    0     0  26916      0 --:--:-- --:--:-- --:--:-- 26916\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mCOMBINE/OMEX archive has warnings.\r\n  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 2\n      Skipped: 0\n      Failed: 0\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 2 SED documents:\n  SED documents (2):\n    Succeeded: 2\n    Skipped: 0\n    Failed: 0\n  Tasks (2):\n    Succeeded: 2\n    Skipped: 0\n    Failed: 0\n  Outputs (4):\n    Succeeded: 4\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/readme.txt     \n  inflating: contents/continuations.ode  \n  inflating: contents/time_series.ode  \n  inflating: contents/continuations.sedml  \n  inflating: contents/time_series.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 7.7 KiB/51.9 KiB (112.9 KiB/s) with 7 file(s) remaining\rupload: contents/continuations.sedml to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/contents/continuations.sedml\nCompleted 7.7 KiB/51.9 KiB (112.9 KiB/s) with 6 file(s) remaining\rCompleted 8.5 KiB/51.9 KiB (80.1 KiB/s) with 6 file(s) remaining \rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/contents/manifest.xml\nCompleted 8.5 KiB/51.9 KiB (80.1 KiB/s) with 5 file(s) remaining\rCompleted 16.7 KiB/51.9 KiB (151.5 KiB/s) with 5 file(s) remaining\rupload: contents/continuations.ode to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/contents/continuations.ode\nCompleted 16.7 KiB/51.9 KiB (151.5 KiB/s) with 4 file(s) remaining\rCompleted 34.4 KiB/51.9 KiB (292.1 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/contents/metadata.rdf\nCompleted 34.4 KiB/51.9 KiB (292.1 KiB/s) with 3 file(s) remaining\rCompleted 40.2 KiB/51.9 KiB (278.8 KiB/s) with 3 file(s) remaining\rupload: contents/time_series.ode to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/contents/time_series.ode\nCompleted 40.2 KiB/51.9 KiB (278.8 KiB/s) with 2 file(s) remaining\rCompleted 49.0 KiB/51.9 KiB (333.8 KiB/s) with 2 file(s) remaining\rupload: contents/time_series.sedml to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/contents/time_series.sedml\nCompleted 49.0 KiB/51.9 KiB (333.8 KiB/s) with 1 file(s) remaining\rCompleted 51.9 KiB/51.9 KiB (331.1 KiB/s) with 1 file(s) remaining\rupload: contents/readme.txt to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/contents/readme.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /continuations.sedml\ncreating dataset /continuations.sedml/plot, shape: (4, 1001), type: float64\ndataset created, uuid: d-d0af774b-e1ee5d37-5e54-79a04a-d108ea, chunk_size: (4, 1001)\ncreating dataset /continuations.sedml/report, shape: (15, 1001), type: float64\ndataset created, uuid: d-d0af774b-e1ee5d37-6f7b-d2cb6f-7d4ef7, chunk_size: (15, 1001)\ncreating group /time_series.sedml\ncreating dataset /time_series.sedml/plot, shape: (5, 1001), type: float64\ndataset created, uuid: d-d0af774b-e1ee5d37-94c6-b77d5d-032f1e, chunk_size: (5, 1001)\ncreating dataset /time_series.sedml/report, shape: (17, 1001), type: float64\ndataset created, uuid: d-d0af774b-e1ee5d37-dcd6-b063ef-09cfb0, chunk_size: (17, 1001)\ncreating attribute combineArchiveLocation in /continuations.sedml\ncreating attribute uri in /continuations.sedml\ncreating attribute _type in /continuations.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /continuations.sedml/plot\ncreating attribute sedmlDataSetIds in /continuations.sedml/plot\ncreating attribute sedmlDataSetLabels in /continuations.sedml/plot\ncreating attribute sedmlDataSetNames in /continuations.sedml/plot\ncreating attribute sedmlDataSetShapes in /continuations.sedml/plot\ncreating attribute sedmlId in /continuations.sedml/plot\ncreating attribute uri in /continuations.sedml/plot\ncreating attribute _type in /continuations.sedml/report\ncreating attribute sedmlDataSetDataTypes in /continuations.sedml/report\ncreating attribute sedmlDataSetIds in /continuations.sedml/report\ncreating attribute sedmlDataSetLabels in /continuations.sedml/report\ncreating attribute sedmlDataSetNames in /continuations.sedml/report\ncreating attribute sedmlDataSetShapes in /continuations.sedml/report\ncreating attribute sedmlId in /continuations.sedml/report\ncreating attribute sedmlName in /continuations.sedml/report\ncreating attribute uri in /continuations.sedml/report\ncreating attribute combineArchiveLocation in /time_series.sedml\ncreating attribute uri in /time_series.sedml\ncreating attribute _type in /time_series.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /time_series.sedml/plot\ncreating attribute sedmlDataSetIds in /time_series.sedml/plot\ncreating attribute sedmlDataSetLabels in /time_series.sedml/plot\ncreating attribute sedmlDataSetNames in /time_series.sedml/plot\ncreating attribute sedmlDataSetShapes in /time_series.sedml/plot\ncreating attribute sedmlId in /time_series.sedml/plot\ncreating attribute uri in /time_series.sedml/plot\ncreating attribute _type in /time_series.sedml/report\ncreating attribute sedmlDataSetDataTypes in /time_series.sedml/report\ncreating attribute sedmlDataSetIds in /time_series.sedml/report\ncreating attribute sedmlDataSetLabels in /time_series.sedml/report\ncreating attribute sedmlDataSetNames in /time_series.sedml/report\ncreating attribute sedmlDataSetShapes in /time_series.sedml/report\ncreating attribute sedmlId in /time_series.sedml/report\ncreating attribute sedmlName in /time_series.sedml/report\ncreating attribute uri in /time_series.sedml/report\ncreate_links: /\ngot link: continuations.sedml\ngot link: time_series.sedml\ncreate_links: /continuations.sedml\ngot link: plot\ngot link: report\ncreate_links: /time_series.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /continuations.sedml/plot to tgt: /continuations.sedml/plot, shape: (4, 1001), type: float64\niterating over chunks for /continuations.sedml/plot\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /continuations.sedml/plot\nwrite_dataset src: /continuations.sedml/report to tgt: /continuations.sedml/report, shape: (15, 1001), type: float64\niterating over chunks for /continuations.sedml/report\nwriting dataset data for slice: (slice(0, 15, 1), slice(0, 1001, 1))\ndone with dataload for /continuations.sedml/report\nwrite_dataset src: /time_series.sedml/plot to tgt: /time_series.sedml/plot, shape: (5, 1001), type: float64\niterating over chunks for /time_series.sedml/plot\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /time_series.sedml/plot\nwrite_dataset src: /time_series.sedml/report to tgt: /time_series.sedml/report, shape: (17, 1001), type: float64\niterating over chunks for /time_series.sedml/report\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /time_series.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42b5b50991044c79ade0\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/continuations.sedml/ (stored 0%)\n  adding: outputs/continuations.sedml/plot.pdf (deflated 36%)\n  adding: outputs/time_series.sedml/ (stored 0%)\n  adding: outputs/time_series.sedml/plot.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 24%)\n  adding: rawLog.txt (deflated 81%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 148.5 KiB/186.2 KiB (1.9 MiB/s) with 5 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/output.zip\nCompleted 148.5 KiB/186.2 KiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 160.0 KiB/186.2 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/outputs/plots.zip\nCompleted 160.0 KiB/186.2 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 167.9 KiB/186.2 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: outputs/continuations.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/outputs/continuations.sedml/plot.pdf\nCompleted 167.9 KiB/186.2 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 177.3 KiB/186.2 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: outputs/time_series.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/outputs/time_series.sedml/plot.pdf\nCompleted 177.3 KiB/186.2 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 186.2 KiB/186.2 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/rawLog.txt\nCompleted 174.2 KiB/174.2 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/outputs/reports.h5\nCompleted 7.1 KiB/7.1 KiB (120.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42b5b50991044c79ade0/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}